814 research outputs found
Effects of Cultural Practices on Total Phenolics and Vitamin C Content of Organic Table Grapes
The total phenolic and vitamin C contents of organic table grapes were determined by spectrophotometry and HPLC, respectively, after several quality-increasing treatments were applied at véraison for two growing seasons. Cane girdling and cluster-berry thinning resulted in different responses in the cultivars. ‘Red Globe’ generally was found to produce the lowest quantity of total phenolics in the berries, while ‘Trakya Ilkeren’ was the cultivar that accumulated the highest phenolics. Vitamin C accumulation in the berries was also affected by the treatments. The effect of the treatments was inconclusive in ‘Buca Razakısı’. The application of both girdling and thinning caused more accumulation of vitamin C in the ‘Alphonse L.’ and ‘Trakya Ilkeren’ berries
A Jupiter-mass planet around the K0 giant HD 208897
For over 10 years, we have carried out a precise radial velocity (RV) survey
to find substellar companions around evolved G,K-type stars to extend our
knowledge of planet formation and evolution. We performed high precision RV
measurements for the giant star HD 208897 using an iodine (I2) absorption cell.
The measurements were made at T\"UB\.ITAK National Observatory (TUG, RTT150)
and Okayama Astrophysical Observatory (OAO). For the origin of the periodic
variation seen in the RV data of the star, we adopted a Keplerian motion caused
by an unseen companion. We found that the star hosts a planet with a minimum
mass of m2sini=1.40MJ, which is relatively low compared to those of known
planets orbiting evolved intermediate-mass stars. The planet is in a nearly
circular orbit with a period of P=353 days at about 1 AU distance from the host
star. The star is metal rich and located at the early phase of ascent along the
red giant branch. The photometric observations of the star at Ankara University
Kreiken Observatory (AUKR) and the HIPPARCOS photometry show no sign of
variation with periods associated with the RV variation. Neither bisector
velocity analysis nor analysis of the Ca II and Halpha lines shows any
correlation with the RV measurements
Reentrant Phase Transitions of the Blume-Emery-Griffiths Model for a Simple Cubic Lattice on the Cellular Automaton
The spin-1 Ising (BEG) model with the nearest-neighbour bilinear and
biquadratic interactions and single-ion anisotropy is simulated on a cellular
automaton which improved from the Creutz cellular automaton(CCA) for a simple
cubic lattice. The simulations have been made for several sets of parameters
and in the and parameter regions.
The re-entrant and double re-entrant phase transitions of the BEG model are
determined from the temperature variations of the thermodynamic quantities
(, and ). The phase diagrams characterizing phase transitions are
compared with those obtained from other methods.Comment: 12 pages 7 figure
Composite structural motifs of binding sites for delineating biological functions of proteins
Most biological processes are described as a series of interactions between
proteins and other molecules, and interactions are in turn described in terms
of atomic structures. To annotate protein functions as sets of interaction
states at atomic resolution, and thereby to better understand the relation
between protein interactions and biological functions, we conducted exhaustive
all-against-all atomic structure comparisons of all known binding sites for
ligands including small molecules, proteins and nucleic acids, and identified
recurring elementary motifs. By integrating the elementary motifs associated
with each subunit, we defined composite motifs which represent
context-dependent combinations of elementary motifs. It is demonstrated that
function similarity can be better inferred from composite motif similarity
compared to the similarity of protein sequences or of individual binding sites.
By integrating the composite motifs associated with each protein function, we
define meta-composite motifs each of which is regarded as a time-independent
diagrammatic representation of a biological process. It is shown that
meta-composite motifs provide richer annotations of biological processes than
sequence clusters. The present results serve as a basis for bridging atomic
structures to higher-order biological phenomena by classification and
integration of binding site structures.Comment: 34 pages, 7 figure
Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles
The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein-protein interaction prediction and design methods. © 2013 American Chemical Society
Cd81 Interacts with the T Cell Receptor to Suppress Signaling
CD81 (TAPA-1) is a ubiquitously expressed tetraspanin protein identified as a component of the B lymphocyte receptor (BCR) and as a receptor for the Hepatitis C Virus. In an effort to identify trans-membrane proteins that interact with the T-cell antigen receptor (TCR), we performed a membrane yeast two hybrid screen and identified CD81 as an interactor of the CD3delta subunit of the TCR. We found that in the absence of CD81, in thymocytes from knockout mice, TCR engagement resulted in stronger signals. These results were recapitulated in T cell lines that express low levels of CD81 through shRNA mediated silencing. Increased signaling did not result from alterations in the levels of TCR on the surface of T lymphocytes. Although CD81 is not essential for normal T lymphocyte development, it plays an important role in regulating TCR and possibly pre-TCR signal transduction by controlling the strength of signaling. CD81 dependent alterations in thymocyte signaling are evident in increased CD5 expression on CD81 deficient double positive (DP) thymocytes. We conclude that CD81 interacts with the T cell receptor to suppress signaling. © 2012 Cevik et al
Turner syndrome and associated problems in turkish children: A multicenter study
Objective: Turner syndrome (TS) is a chromosomal disorder caused by complete or partial X chromosome monosomy that manifests various clinical features depending on the karyotype and on the genetic background of affected girls. This study aimed to systematically investigate the key clinical features of TS in relationship to karyotype in a large pediatric Turkish patient population. Methods: Our retrospective study included 842 karyotype-proven TS patients aged 0-18 years who were evaluated in 35 different centers in Turkey in the years 2013-2014. Results: The most common karyotype was 45,X (50.7%), followed by 45,X/46,XX (10.8%), 46,X,i(Xq) (10.1%) and 45,X/46,X,i(Xq) (9.5%). Mean age at diagnosis was 10.2±4.4 years. The most common presenting complaints were short stature and delayed puberty. Among patients diagnosed before age one year, the ratio of karyotype 45,X was significantly higher than that of other karyotype groups. Cardiac defects (bicuspid aortic valve, coarctation of the aorta and aortic stenosi) were the most common congenital anomalies, occurring in 25% of the TS cases. This was followed by urinary system anomalies (horseshoe kidney, double collector duct system and renal rotation) detected in 16.3%. Hashimoto’s thyroiditis was found in 11.1% of patients, gastrointestinal abnormalities in 8.9%, ear nose and throat problems in 22.6%, dermatologic problems in 21.8% and osteoporosis in 15.3%. Learning difficulties and/or psychosocial problems were encountered in 39.1%. Insulin resistance and impaired fasting glucose were detected in 3.4% and 2.2%, respectively. Dyslipidemia prevalence was 11.4%. Conclusion: This comprehensive study systematically evaluated the largest group of karyotype-proven TS girls to date. The karyotype distribution, congenital anomaly and comorbidity profile closely parallel that from other countries and support the need for close medical surveillance of these complex patients throughout their lifespan. © Journal of Clinical Research in Pediatric Endocrinology
Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures
Analysis of the geometric properties of a mean-field HP model on a square
lattice for protein structure shows that structures with large number of switch
backs between surface and core sites are chosen favorably by peptides as unique
ground states. Global comparison of model (binary) peptide sequences with
concatenated (binary) protein sequences listed in the Protein Data Bank and the
Dali Domain Dictionary indicates that the highest correlation occurs between
model peptides choosing the favored structures and those portions of protein
sequences containing alpha-helices.Comment: 4 pages, 2 figure
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